Analysis of QTLs for Reproductive Development and Seed Quality Traits in Soybean using Recombinant Inbred Lines

Abstract

Soybean (Glycine max (L.) Merrill) is the most important leguminous crop in the world due to the high contents of protein and oil, and accumulation of various physiologically active substances. However, most of the genomic and economic traits in soybean are quantitative, controlled by multiple genes and easily affected by environmental conditions. Based on recombinant inbred lines (F 8 ), a genetic linkage map with 177 RFLP, 150 SSR, 28 AFLP markers and 5 phenotypic markers was constructed. The map covered a distance of 2663.6 cM of the soybean genome comprising 20 linkage groups. The average distance between two adjacent marker loci was 7.89 cM. In this population, we detected thirty-nine QTLs for all the reproductive development and seed quality traits investigated, that is, three for flowering time (FT1-3), four for maturity (HAV1-4), three for reproductive period (RP1-3), three for seed hardness (RAS1-3), five for viability of seed (VIS1-5), four for germination rate of seed (GRS1-4), five for water absorbability of seed (WAS1-5) and twelve QTLs for seed weight (SWE1-6 and SWH1-6). Out of these QTLs, twenty-eight were detected in nearly the same regions of the linkage map by both IM (interval mapping) and CIM (composite interval mapping) analysis. The proportion of variance explained of these QTLs ranged from 3.4 % to 67.1 %. Epistatic interactions were detected among various QTLs. Especially there was a strong interaction among the effects of FT1 and FT2, and FT1 and FT3. Multiple correlation coefficients between FT1 and FT2, and FT1 and FT3 accounted for 79.6 % and 74.1 % of the phenotypic variation of flowering time, respectively.

Map-Based Cloning of the Gene Associated With the Soybean Maturity Locus E3

“…This phenomenon could be attributed to epistasis between the FT1 and FT3 loci. Statistical analysis showed that the recessive allele, ft1, reduced the effect of the FT3 allele (Yamanaka et al 2000;Watanabe et al 2004). Moreover, an allelism test between Harosoy and 6-22-ft3, both carrying the recessive ft1 (e1) allele, revealed a very small effect in the variation of flowering time (Table 3).…”

“…Of these, the E1, E3, and E4 loci have been suggested to be related to photoperiod sensitivity under various light conditions (Saidon et al 1989;Cober et al 1996b;Abe et al 2003). In previous studies, using the same populations as in this study, three flowering-time quantitative trait loci (QTL)-FT1, FT2, and FT3 loci-were identified and considered to be identical with the maturity loci E1, E2, and E3, respectively (Yamanaka et al 2001;Watanabe et al 2004). Although many loci related to soybean flowering and maturity have been identified, and some candidate genes were recognized using near isogenic lines (NILs) (Tasma and Shoemaker 2003), most of the genes responsible for these loci have not yet been isolated except for the E4 gene.…”

Genetic Redundancy in Soybean Photoresponses Associated With Duplication of the Phytochrome A Gene

“…None of the classical major genes controlling flowering and maturing times that have been mapped so far is located in LG O. Many QTL influencing the flowering and maturing times have been allocated to various LGs (Keim et al 1990;Mansur et al 1993;Lee et al 1996;Orf et al 1999;Tasma et al 2001;Yamanaka et al 2001;Chapman et al 2003;Watanabe et al 2004;Zhang et al 2004;Funatsuki et al 2005;Liu et al 2007). However, only a maturitycontrolling QTL has been located in LG O (Zhang et al 2004).…”

Positional Cloning of the Responsible Genes for Maturity Loci E1, E2 and E3 in Soybean

“…The recessive alleles of the E2 (FT2) locus were perhaps unable to suppress GmFT2a expression and resulted in the early flowering phenotype. There are strong interaction among the effects of E1 (FT1) and E2 (FT2), E1 (FT1) and E3 (FT3) (Yamanaka et al 2000;Watanabe et al 2004). The e3e3 recessive homozygote can initiate flowering under R-enriched LD, but the e3e3 genotype is necessary for plants with e4 mutant allele to flower under FR-enriched LD.…”

“…3). The FT1, FT2 and FT3 were considered to correspond to E1, E2, E3, respectively, based on their map positions (Yamanaka et al, 2001;Watanabe et al, 2004). The lateflowering alleles FT1, FT2 and FT3 are partially dominant over the early-flowering alleles, ft1, ft2 and ft3, respectively.…”